# | Line 73 | Line 73 | SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, | |
---|---|---|
73 | nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), | |
74 | nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), | |
75 | nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), | |
76 | < | sman_(NULL), fortranInitialized_(false), selectMan_(NULL) { |
76 | > | sman_(NULL), fortranInitialized_(false) { |
77 | ||
78 | ||
79 | std::vector<std::pair<MoleculeStamp*, int> >::iterator i; | |
# | Line 139 | Line 139 | SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, | |
139 | molToProcMap_.resize(nGlobalMols_); | |
140 | #endif | |
141 | ||
142 | – | selectMan_ = new SelectionManager(this); |
143 | – | selectMan_->selectAll(); |
142 | } | |
143 | ||
144 | SimInfo::~SimInfo() { | |
145 | < | //MemoryUtils::deleteVectorOfPointer(molecules_); |
146 | < | |
147 | < | MemoryUtils::deleteVectorOfPointer(moleculeStamps_); |
145 | > | std::map<int, Molecule*>::iterator i; |
146 | > | for (i = molecules_.begin(); i != molecules_.end(); ++i) { |
147 | > | delete i->second; |
148 | > | } |
149 | > | molecules_.clear(); |
150 | ||
151 | + | MemoryUtils::deletePointers(moleculeStamps_); |
152 | + | |
153 | delete sman_; | |
154 | delete simParams_; | |
155 | delete forceField_; | |
154 | – | delete selectMan_; |
156 | } | |
157 | ||
158 | int SimInfo::getNGlobalConstraints() { | |
# | Line 366 | Line 367 | void SimInfo::addExcludePairs(Molecule* mol) { | |
367 | exclude_.addPair(c, d); | |
368 | } | |
369 | ||
370 | < | |
370 | > | Molecule::RigidBodyIterator rbIter; |
371 | > | RigidBody* rb; |
372 | > | for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
373 | > | std::vector<Atom*> atoms = rb->getAtoms(); |
374 | > | for (int i = 0; i < atoms.size() -1 ; ++i) { |
375 | > | for (int j = i + 1; j < atoms.size(); ++j) { |
376 | > | a = atoms[i]->getGlobalIndex(); |
377 | > | b = atoms[j]->getGlobalIndex(); |
378 | > | exclude_.addPair(a, b); |
379 | > | } |
380 | > | } |
381 | > | } |
382 | > | |
383 | } | |
384 | ||
385 | void SimInfo::removeExcludePairs(Molecule* mol) { | |
# | Line 411 | Line 424 | void SimInfo::removeExcludePairs(Molecule* mol) { | |
424 | exclude_.removePair(c, d); | |
425 | } | |
426 | ||
427 | + | Molecule::RigidBodyIterator rbIter; |
428 | + | RigidBody* rb; |
429 | + | for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
430 | + | std::vector<Atom*> atoms = rb->getAtoms(); |
431 | + | for (int i = 0; i < atoms.size() -1 ; ++i) { |
432 | + | for (int j = i + 1; j < atoms.size(); ++j) { |
433 | + | a = atoms[i]->getGlobalIndex(); |
434 | + | b = atoms[j]->getGlobalIndex(); |
435 | + | exclude_.removePair(a, b); |
436 | + | } |
437 | + | } |
438 | + | } |
439 | + | |
440 | } | |
441 | ||
442 | ||
# | Line 645 | Line 671 | void SimInfo::setupFortranSim() { | |
671 | } | |
672 | ||
673 | //setup fortran simulation | |
648 | – | //gloalExcludes and molMembershipArray should go away (They are never used) |
649 | – | //why the hell fortran need to know molecule? |
650 | – | //OOPSE = Object-Obfuscated Parallel Simulation Engine |
674 | int nGlobalExcludes = 0; | |
675 | int* globalExcludes = NULL; | |
676 | int* excludeList = exclude_.getExcludeList(); | |
# | Line 765 | Line 788 | void SimInfo::getCutoff(double& rcut, double& rsw) { | |
788 | "\tfor the cutoffRadius.\n"); | |
789 | painCave.isFatal = 0; | |
790 | simError(); | |
791 | < | rcut_ = 15.0; |
791 | > | rcut = 15.0; |
792 | } else{ | |
793 | < | rcut_ = simParams_->getRcut(); |
793 | > | rcut = simParams_->getRcut(); |
794 | } | |
795 | ||
796 | if (!simParams_->haveRsw()){ | |
# | Line 777 | Line 800 | void SimInfo::getCutoff(double& rcut, double& rsw) { | |
800 | "\t0.95 * cutoffRadius for the switchingRadius\n"); | |
801 | painCave.isFatal = 0; | |
802 | simError(); | |
803 | < | rsw_ = 0.95 * rcut_; |
803 | > | rsw = 0.95 * rcut; |
804 | } else{ | |
805 | < | rsw_ = simParams_->getRsw(); |
805 | > | rsw = simParams_->getRsw(); |
806 | } | |
807 | ||
808 | } else { | |
# | Line 787 | Line 810 | void SimInfo::getCutoff(double& rcut, double& rsw) { | |
810 | //meta-data file, the maximum cutoff radius calculated from forcefiled will be used | |
811 | ||
812 | if (simParams_->haveRcut()) { | |
813 | < | rcut_ = simParams_->getRcut(); |
813 | > | rcut = simParams_->getRcut(); |
814 | } else { | |
815 | //set cutoff radius to the maximum cutoff radius based on atom types in the whole system | |
816 | < | rcut_ = calcMaxCutoffRadius(); |
816 | > | rcut = calcMaxCutoffRadius(); |
817 | } | |
818 | ||
819 | if (simParams_->haveRsw()) { | |
820 | < | rsw_ = simParams_->getRsw(); |
820 | > | rsw = simParams_->getRsw(); |
821 | } else { | |
822 | < | rsw_ = rcut_; |
822 | > | rsw = rcut; |
823 | } | |
824 | ||
825 | } | |
# | Line 835 | Line 858 | void SimInfo::setSnapshotManager(SnapshotManager* sman | |
858 | } | |
859 | ||
860 | void SimInfo::setSnapshotManager(SnapshotManager* sman) { | |
861 | + | if (sman_ == sman) { |
862 | + | return; |
863 | + | } |
864 | + | delete sman_; |
865 | sman_ = sman; | |
866 | ||
867 | Molecule* mol; |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |